Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011967.1 Corchorus capsularis cultivar CVL-1 contig11988, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 11765
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Found at i:1094 original size:27 final size:27
Alignment explanation
Indices: 1056--1138 Score: 112
Period size: 27 Copynumber: 3.1 Consensus size: 27
1046 GGAGCGTGAG
*
1056 GGTGGTGACGTTCTTCACACCCTTGTA
1 GGTGGCGACGTTCTTCACACCCTTGTA
* *
1083 GGTGGGGACGTTCTTCACACCCTTGGA
1 GGTGGCGACGTTCTTCACACCCTTGTA
* * *
1110 GGTGACGAAGTTCGTCACACCCTTGTA
1 GGTGGCGACGTTCTTCACACCCTTGTA
1137 GG
1 GG
1139 AATGTGATCA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.17, C:0.25, G:0.30, T:0.28
Consensus pattern (27 bp):
GGTGGCGACGTTCTTCACACCCTTGTA
Found at i:4429 original size:2 final size:2
Alignment explanation
Indices: 4422--4449 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4412 TGCAACATCA
4422 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
4450 ACTTTGAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:8267 original size:45 final size:45
Alignment explanation
Indices: 8203--8295 Score: 134
Period size: 45 Copynumber: 2.1 Consensus size: 45
8193 ATCCGTCCAA
* *
8203 GCCCGTAAGCCTGCCCCATATTTAACCA-TCCAAGCCCGTAAGCTT
1 GCCCGCAAACCTGCCCCATATTTAA-CAGTCCAAGCCCGTAAGCTT
* *
8248 GCCCGCAAACCTGCCCCATATTTAACAGTGCAAGCCCGTAAGTTT
1 GCCCGCAAACCTGCCCCATATTTAACAGTCCAAGCCCGTAAGCTT
8293 GCC
1 GCC
8296 AGATATTTAG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 2 0.05
45 41 0.95
ACGTcount: A:0.25, C:0.37, G:0.17, T:0.22
Consensus pattern (45 bp):
GCCCGCAAACCTGCCCCATATTTAACAGTCCAAGCCCGTAAGCTT
Found at i:8302 original size:33 final size:33
Alignment explanation
Indices: 8265--8327 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
8255 AACCTGCCCC
*
8265 ATATTTAACAGTGCAAGCCCGTAAGTTTGCCAG
1 ATATTTAACAGTCCAAGCCCGTAAGTTTGCCAG
* * *
8298 ATATTTAGCCGTCCAAGCCTGTAAGTTTGC
1 ATATTTAACAGTCCAAGCCCGTAAGTTTGC
8328 TCGGTTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (33 bp):
ATATTTAACAGTCCAAGCCCGTAAGTTTGCCAG
Found at i:8858 original size:245 final size:245
Alignment explanation
Indices: 8423--8969 Score: 1006
Period size: 245 Copynumber: 2.2 Consensus size: 245
8413 CGGGCTTGGG
* **
8423 TATTGTTTATGAGTATTGTGGCTAAACATTAAGGAAAAATCATTCGAGTCAATTTTAGCCGAAAT
1 TATTTTTTATGAACATTGTGGCTAAACATTAAGGAAAAATCATTCGAGTCAATTTTAGCCGAAAT
8488 CGATACGTTAAATCATTGGTTATTTTGCTAAAAGCTCATTCCGTGGTCCCAGCTCAATTTTGCAT
66 CGATACGTTAAATCATTGGTTATTTTGCTAAAAGCTCATTCCGTGGTCCCAGCTCAATTTTGCAT
8553 GATTTTTTTGGGCCAAGACTCCTTTAAAAAATCTATATTCATCTAACCAAATAGGAAAAACGATA
131 GATTTTTTTGGGCCAAGACTCCTTTAAAAAATCTATATTCATCTAACCAAATAGGAAAAACGATA
8618 TTAGACACGCGAAAGAACCTTAAATTATTTTGGCATTAAATTTTTTTATA
196 TTAGACACGCGAAAGAACCTTAAATTATTTTGGCATTAAATTTTTTTATA
8668 TATTTTTTATGAACATTGTGGCTAAACATTAAGGAAAAATCATTCGAGTCAATTTTAGCCGAAAT
1 TATTTTTTATGAACATTGTGGCTAAACATTAAGGAAAAATCATTCGAGTCAATTTTAGCCGAAAT
8733 CGATACGTTAAATCATTGGTTATTTTGCTAAAAGCTCATTCCGTGGTCCCAGCTCAATTTTGCAT
66 CGATACGTTAAATCATTGGTTATTTTGCTAAAAGCTCATTCCGTGGTCCCAGCTCAATTTTGCAT
8798 GATTTTTTTGGGCCAAGACTCCTTTAAAAAATCTATATTCATCTAACCAAATAGGAAAAACGATA
131 GATTTTTTTGGGCCAAGACTCCTTTAAAAAATCTATATTCATCTAACCAAATAGGAAAAACGATA
8863 TTAGACACGCGAAAGAACCTTAAATTATTTTGGCATTAAATTTTTTTATA
196 TTAGACACGCGAAAGAACCTTAAATTATTTTGGCATTAAATTTTTTTATA
* * * *
8913 TATTTTTTATGAACATTGTGGCTATAAC-TTGAGGAAAAACCTTTCAGTGTCAATTTT
1 TATTTTTTATGAACATTGTGGCTA-AACATTAAGGAAAAATCATTC-GAGTCAATTTT
8970 TGCAAAATTA
Statistics
Matches: 293, Mismatches: 7, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
245 280 0.96
246 13 0.04
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (245 bp):
TATTTTTTATGAACATTGTGGCTAAACATTAAGGAAAAATCATTCGAGTCAATTTTAGCCGAAAT
CGATACGTTAAATCATTGGTTATTTTGCTAAAAGCTCATTCCGTGGTCCCAGCTCAATTTTGCAT
GATTTTTTTGGGCCAAGACTCCTTTAAAAAATCTATATTCATCTAACCAAATAGGAAAAACGATA
TTAGACACGCGAAAGAACCTTAAATTATTTTGGCATTAAATTTTTTTATA
Found at i:10172 original size:39 final size:40
Alignment explanation
Indices: 10118--10194 Score: 129
Period size: 39 Copynumber: 1.9 Consensus size: 40
10108 TTTGTTTTCT
10118 GCTTTTCTTTGCTCTTCATTG-TTATGGTTAGCTGAATTG
1 GCTTTTCTTTGCTCTTCATTGTTTATGGTTAGCTGAATTG
* *
10157 GCTTTTTTTTGCTCTTCATTGTTTATGGTTAGGTGAAT
1 GCTTTTCTTTGCTCTTCATTGTTTATGGTTAGCTGAAT
10195 CGAAGCACTG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 20 0.57
40 15 0.43
ACGTcount: A:0.13, C:0.13, G:0.21, T:0.53
Consensus pattern (40 bp):
GCTTTTCTTTGCTCTTCATTGTTTATGGTTAGCTGAATTG
Found at i:11053 original size:324 final size:324
Alignment explanation
Indices: 10418--11213 Score: 818
Period size: 324 Copynumber: 2.4 Consensus size: 324
10408 TTTACGAGTT
* * * ** *
10418 TCAGAATCATGTTTCGATTTAATTAAAATTTAATTCGAAAAAAAAATAAAAACAATATTAGAAGC
1 TCAGAACCATGTTTCGATTTAATTAAAAATTAATTAGAAAAAAAAGGAAAAACAATATTAGAAAC
* **
10483 GTGAAAAACCCTTCAATCTTTTTGACCTTGAATTATATATTCTTTTATGAGTATTATGGCCAAAA
66 GTGAAAAGCCCTTCAAT-TTTTTGAAGTTGAATTATATATTCTTTTATGAGTATTATGGCCAAAA
* *
10548 ATTGAGGAAAAATTTTTTAGGTCAATTTTTTAAAATTTTAGCCAAAATCGTGTACTAACCATAAC
130 ATTGAGGAAAAATCTTTCAGGTCAA----TT---ATTTTAGCCAAAATCGTGTACTAACCAT-AC
* * * * * * *
10613 ATTTTTTTTTGCTAAAAACGTGTTCCGGGGACCTAGCTAAATTTCGCATGAATTTTGGCGCCATG
187 ACTGTTTTTGGCTAAAAACGTGTTCCGGAGACCCAGCTAAATTTCGCATGAATTTTAGCGCCAAG
* * * ** * *
10678 ACTCCTTGAAATATCAATTTTAATCTAACCTAATCTCAGCCATATTGGATTTAAGGATTTGTTTT
252 ACTCCATGAAATATCAATATAAATCTAACAAAATCTCAGCCACATTGGATTTAAAGATTTGTTTT
*
10743 AATGAGCA
317 AACGAGCA
** *
10751 TCAGAACCGA-GTTTCGATTTAATTAAAAATTAATTAGAAAAAAATAGGAAAAATGATATTATAA
1 TCAGAACC-ATGTTTCGATTTAATTAAAAATTAATTAGAAAAAAA-AGGAAAAACAATATTAGAA
** * *
10815 ACGTGAAAAGCCCTTCAATATTTTTGTTGTTGAATTATATATATATTTTTATGAGTA-TACTGTC
64 ACGTGAAAAGCCCTTCAAT-TTTTTGAAGTTGAATTATATAT-T-CTTTTATGAGTATTA-TGGC
* * *
10879 TAAAAATTGTGGAAAAATCTTTCGGGTCAA-T-TTTT-GCCAAAATCGTGTACTAACCAT-CACT
125 CAAAAATTGAGGAAAAATCTTTCAGGTCAATTATTTTAGCCAAAATCGTGTACTAACCATACACT
* * * * *
10940 GTTTTTGGCTAAAAACAG-GTTCTGGAGCCCCGGCTCAATGTT-GCATGATTTTTAGCGCCAAGA
190 GTTTTTGGCTAAAAAC-GTGTTCCGGAGACCCAGCTAAAT-TTCGCATGAATTTTAGCGCCAAGA
* * *
11003 TTCCATGAAATATCTATATAAATCTAACAAAATCTCAGCCACATTGGATTTAAAGATTTGTTTTT
253 CTCCATGAAATATCAATATAAATCTAACAAAATCTCAGCCACATTGGATTTAAAGATTTGTTTTA
11068 ACGAGCA
318 ACGAGCA
* * * * * * *
11075 TCTGAATCATGTTTCGATTTAATTAGAAATGAATTCGGGTAAACAAAAGGAAAAACAATATCAGA
1 TCAGAACCATGTTTCGATTTAATTAAAAATTAATT--AG-AAAAAAAAGGAAAAACAATATTAGA
* * * * ** * *
11140 AACGTGAAAAGTCCTTCAATTATTTGGAGGTGAATTATATATTC-TTTATGAGTATTGCGACTAA
63 AACGTGAAAAGCCCTTCAATTTTTTGAAGTTGAATTATATATTCTTTTATGAGTATTATGGCCAA
11204 AAATTGAGGA
128 AAATTGAGGA
11214 TTTGTTTTTA
Statistics
Matches: 387, Mismatches: 64, Indels: 35
0.80 0.13 0.07
Matches are distributed among these distances:
322 24 0.06
323 2 0.01
324 141 0.36
325 21 0.05
326 56 0.14
327 10 0.03
331 1 0.00
333 39 0.10
334 51 0.13
335 3 0.01
336 39 0.10
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (324 bp):
TCAGAACCATGTTTCGATTTAATTAAAAATTAATTAGAAAAAAAAGGAAAAACAATATTAGAAAC
GTGAAAAGCCCTTCAATTTTTTGAAGTTGAATTATATATTCTTTTATGAGTATTATGGCCAAAAA
TTGAGGAAAAATCTTTCAGGTCAATTATTTTAGCCAAAATCGTGTACTAACCATACACTGTTTTT
GGCTAAAAACGTGTTCCGGAGACCCAGCTAAATTTCGCATGAATTTTAGCGCCAAGACTCCATGA
AATATCAATATAAATCTAACAAAATCTCAGCCACATTGGATTTAAAGATTTGTTTTAACGAGCA
Found at i:11605 original size:21 final size:21
Alignment explanation
Indices: 11589--11643 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
11579 AGGAAGTGAT
11589 TTAGACAAAAAGAGAAGCAAC
1 TTAGACAAAAAGAGAAGCAAC
*
11610 TTGGACAAAAAGAGAAGCAAC
1 TTAGACAAAAAGAGAAGCAAC
*
11631 TTGGACAAAAAGA
1 TTAGACAAAAAGA
11644 AACGAAGTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.55, C:0.13, G:0.22, T:0.11
Consensus pattern (21 bp):
TTAGACAAAAAGAGAAGCAAC
Done.